This ReMatCh repository, and specially the antibiotics_book_chapter branch (https://github.com/miguelpmachado/ReMatCh/tree/antibiotics_book_chapter) is only kept for use illustration in "Epidemiological Surveillance and Typing Methods to Track Antibiotic Resistant Strains Using High Throughput Sequencing" chapter from Antibiotics - Methods and Protocols book (Methods Molecular Biology Series, Springer, 2016).
Therefore, It will not be subject to further updates!
The recent and supported ReMatCh repository can be found at https://github.com/B-UMMI/ReMatCh